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Asano A, Kawanami Y, Fujita M, Yano Y, Ide R, Minoura K, Kato T, Doi M. Electronic substituent effect on the conformation of a phenylalanine-incorporated cyclic peptide. RSC Adv 2024; 14:1062-1071. [PMID: 38174232 PMCID: PMC10759965 DOI: 10.1039/d3ra07836a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
The Phe-incorporated cyclic peptide [cyclo(-Phe1-oxazoline2-d-Val3-thiazole4-Ile5-oxazoline6-d-Val7-thiazole8-)] is in a conformational equilibrium between square and folded forms in solution. In the folded form, a CH⋯π interaction between the Phe1 aromatic ring and the Oxz2 methyl group is observed. We endeavored to control the local conformation and thus modulate the CH⋯π interaction and flexibility of the Phe1 side chain by controlling the electronic substituent effects at the 4-position of the aromatic ring of the Phe1 residue. The effect of the 4-substituent on the global conformation was indicated by the linear relationship between the conformational free energies (ΔGo) determined through NMR-based quantification and the Hammett constants (σ). Electron-donating substituents, which had relatively strong CH⋯π interactions, promoted peptide folding by restraining the loss in entropy. Local control by the 4-substituent effects suggested that the Phe side chain exerts an entropic influence on the folding of these cyclic peptides.
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Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Yukiko Kawanami
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Mao Fujita
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Yuta Yano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Rio Ide
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Katsuhiko Minoura
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University 4-20-1 Nasahara, Takatsuki Osaka 569-1094 Japan +81-72-690-1005 +81-72-690-1066
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2
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Asano A, Minoura K, Yamada T, Doi M. Experimental evidence for CH⋯π interaction-mediated stabilization of the square form in phenylglycine-incorporated ascidiacyclamide. RSC Adv 2023; 13:2458-2466. [PMID: 36741171 PMCID: PMC9854340 DOI: 10.1039/d2ra07063d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Ascidiacyclamide [cyclo(-Ile-oxazoline-D-Val-thiazole-)2] is a cytotoxic cyclic peptide from ascidian. We examined the potential of the CH⋯π interaction at the diagonal position of ascidiacyclamide by comparing the interactions of Ile, Val, Abu (2-aminobutyric acid) or Ala with Ile, Chg (cyclohexylglycine) or Phg (phenylglycine). In solution, ascidiacyclamides are in a conformational equilibrium between square and folded forms. The CH⋯π interaction is expected to contribute to stabilization of the square form, which enhances the peptides' cytotoxicity. The distances between the alkyl side chain of Xaa and the π-plane of Phg were estimated from the crystal structures. The conformational free energies (ΔG°) determined through NMR-based quantitation indicated remarkable stabilization of the square form upon incorporation of Phg. These observations were consistent with the circular dichroism (CD) spectral measurements. Chemical shift perturbation studies suggested that stabilization of the square form of Phg-incorporated peptides was due to the CH⋯π interaction with the alkyl side chain of Xaa. Greater enthalpic losses were caused during the folding process of Phg-incorporated peptides than Ile- or Chg-incorporated peptides. It is suggested that these enthalpic losses are relevant to the CH⋯π interaction energies, which must be disrupted during folding. In addition, the CH⋯π interactions in the Phg-incorporated peptides increased cytotoxicity.
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Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University4-20-1 NasaharaTakatsukiOsaka 569-1094Japan+81-72-690-1005+81-72-690-1066
| | - Katsuhiko Minoura
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University4-20-1 NasaharaTakatsukiOsaka 569-1094Japan+81-72-690-1005+81-72-690-1066
| | - Takeshi Yamada
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University4-20-1 NasaharaTakatsukiOsaka 569-1094Japan+81-72-690-1005+81-72-690-1066
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University4-20-1 NasaharaTakatsukiOsaka 569-1094Japan+81-72-690-1005+81-72-690-1066
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3
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Kumar S, Borish K, Dey S, Nagesh J, Das A. Sequence dependent folding motifs of the secondary structures of Gly-Pro and Pro-Gly containing oligopeptides. Phys Chem Chem Phys 2022; 24:18408-18418. [PMID: 35880873 DOI: 10.1039/d2cp01306a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Folding motifs of the secondary structures of peptides and proteins are primarily based on the hydrogen bonding interactions in the backbone as well as the sequence of the amino acid residues present. For instance, the β-turn structure directed by the Pro-Gly sequence is the key to the β-hairpin structure of peptides/proteins as well as a selective site for the enzymatic hydroxylation of pro-collagen. Herein, we have investigated the sequence dependent folding motifs of end-protected Gly-Pro and Pro-Gly dipeptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). All three observed conformers of the Gly-Pro peptide in the gas phase have been found to have extended β-strand or polyproline-II (PP-II) structures with C5-C7 hydrogen bonding interactions, which correlates well with the structure obtained from solution phase spectroscopy and XRD. On the other hand, we have found that the Pro-Gly peptide has a C10/β-turn structure in the solution phase in contrast to the C7-C7 (i.e. 27-ribbon) structure observed in the gas phase. Although the lowest energy structure in the gas phase is not C10, we find that C7-C7 is an abundantly found structural motif of Pro-Gly containing peptides in the Cambridge Structural Database, indicating that the gas phase conformers are not sampling any unusual forms. We surmise that the role of the solvent could be crucial in dictating the preferential stabilization of the C10 structure in the solution phase. The present investigation provides a comprehensive picture of the folding motifs of the Gly-Pro and Pro-Gly peptides observed in the gas phase and condensed phase weaving a fine interplay of the intrinsic conformational properties, solvation, and crystal packing of the peptides.
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Affiliation(s)
- Satish Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
| | - Jayashree Nagesh
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India.
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr Homi Bhabha Road, Pashan, Pune-411008, India.
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4
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Lidskog A, Dawaigher S, Solano Arribas C, Ryberg A, Jensen J, Bergquist KE, Sundin A, Norrby PO, Wärnmark K. Experimental and Computational Models for Side Chain Discrimination in Peptide-Protein Interactions. Chemistry 2021; 27:10883-10897. [PMID: 33908678 PMCID: PMC8362025 DOI: 10.1002/chem.202100890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Indexed: 12/02/2022]
Abstract
A bis(18‐crown‐6) Tröger's base receptor and 4‐substituted hepta‐1,7‐diyl bisammonium salt ligands have been used as a model system to study the interactions between non‐polar side chains of peptides and an aromatic cavity of a protein. NMR titrations and NOESY/ROESY NMR spectroscopy were used to analyze the discrimination of the ligands by the receptor based on the substituent of the ligand, both quantitatively (free binding energies) and qualitatively (conformations). The analysis showed that an all‐anti conformation of the heptane chain was preferred for most of the ligands, both free and when bound to the receptor, and that for all of the receptor‐ligand complexes, the substituent was located inside or partly inside of the aromatic cavity of the receptor. We estimated the free binding energy of a methyl‐ and a phenyl group to an aromatic cavity, via CH‐π, and combined aromatic CH‐π and π‐π interactions to be −1.7 and −3.3 kJ mol−1, respectively. The experimental results were used to assess the accuracy of different computational methods, including molecular mechanics (MM) and density functional theory (DFT) methods, showing that MM was superior.
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Affiliation(s)
- Anna Lidskog
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Sami Dawaigher
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Carlos Solano Arribas
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anna Ryberg
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Jacob Jensen
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Karl Erik Bergquist
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Anders Sundin
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
| | - Per-Ola Norrby
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Kenneth Wärnmark
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P. O Box 124, S-221 00, Lund, Sweden
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5
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Bhattacharya I, Sadhukhan J, Biswas S, Chakraborty T. Medium-Dependent Crossover from the Red to Blue Shift of the Donor’s Stretching Fundamental in the Binary Hydrogen-Bonded Complexes of CDCl3 with Ethers and Ketones. J Phys Chem A 2020; 124:7259-7270. [DOI: 10.1021/acs.jpca.0c03946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Indrani Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Jayshree Sadhukhan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
- Department of Chemistry, Govt. General Degree College, Singur, Hooghly 712409, West Bengal, India
| | - Souvick Biswas
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Tapas Chakraborty
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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6
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Gorla L, Martí-Centelles V, Altava B, Burguete MI, Luis SV. The role of the side chain in the conformational and self-assembly patterns of C2-symmetric Val and Phe pseudopeptidic derivatives. CrystEngComm 2019. [DOI: 10.1039/c8ce02088d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Side chain as the main conformational and self-assembly structural factor for C2-pseudopeptides.
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Affiliation(s)
- Lingaraju Gorla
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | | | - Belén Altava
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - M. Isabel Burguete
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
| | - Santiago V. Luis
- Departamento de Química Inorgánica y Orgánica
- Universitat Jaume I
- Castellón
- Spain
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7
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Nakao M. Development of Novel Functional Molecules Based on the Molecular Structure Characteristics of Diketopiperazines. YAKUGAKU ZASSHI 2017; 137:1505-1516. [DOI: 10.1248/yakushi.17-00176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Michiyasu Nakao
- Graduate School of Pharmaceutical Sciences, Tokushima University
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8
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Gopi R, Ramanathan N, Sundararajan K. Experimental evidence for the blue-shifted hydrogen-bonded complexes of CHF 3 with π-electron donors. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:137-147. [PMID: 28351820 DOI: 10.1016/j.saa.2017.03.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/10/2017] [Accepted: 03/20/2017] [Indexed: 06/06/2023]
Abstract
Blue-shifted hydrogen-bonded complexes of fluoroform (CHF3) with benzene (C6H6) and acetylene (C2H2) have been investigated using matrix isolation infrared spectroscopy and ab initio computations. For CHF3-C6H6 complex, calculations performed at the B3LYP and MP2 levels of theory using 6-311++G (d,p) and aug-cc-pVDZ basis sets discerned two minima corresponding to a 1:1 hydrogen-bonded complex. The global minimum correlated to a structure, where the interaction is between the hydrogen of CHF3 and the π-electrons of C6H6 and a weak local minimum was stabilized through H…F interaction. For the CHF3-C2H2 complex, computation performed at MP2/aug-cc-pVDZ level of theory yielded two minima, corresponding to the cyclic C-H…π complex A (global) and a linear C-H…F (n-σ) complex B (local). Experimentally a blue-shift of 32.3cm-1 and 7.7cm-1 was observed in the ν1 C-H stretching mode of CHF3 sub-molecule in Ar matrix for the 1:1 C-H…π complexes of CHF3 with C6H6 and C2H2 respectively. Natural bond orbital (NBO), Atoms-in-molecule (AIM) and energy decomposition (EDA) analyses were carried out to explain the blue-shifting and the nature of the interaction in these complexes.
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Affiliation(s)
- R Gopi
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India; Homi Bhabha National Institute, Kalpakkam 603102, India
| | - N Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - K Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India; Homi Bhabha National Institute, Kalpakkam 603102, India.
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9
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Ozawa M, Ozawa T, Nishio M, Ueda K. The role of CH/π interactions in the high affinity binding of streptavidin and biotin. J Mol Graph Model 2017; 75:117-124. [PMID: 28551501 DOI: 10.1016/j.jmgm.2017.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/27/2017] [Accepted: 05/02/2017] [Indexed: 11/28/2022]
Abstract
The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 1015mol-1) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.
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Affiliation(s)
- Motoyasu Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan.
| | - Tomonaga Ozawa
- Central Research Laboratory, Kissei Pharmaceutical Co., Ltd., 4365-1 Hotakakashiwabara, Azumino, Nagano 399-8304, Japan
| | | | - Kazuyoshi Ueda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-Ku, Yokohama 240-8501, Japan
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10
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Synthesis, Crystal Structures and Properties of Ferrocenyl Bis-Amide Derivatives Yielded via the Ugi Four-Component Reaction. Molecules 2017; 22:molecules22050737. [PMID: 28471375 PMCID: PMC6154595 DOI: 10.3390/molecules22050737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 11/30/2022] Open
Abstract
Ten ferrocenyl bis-amide derivatives were successfully synthesized via the Ugi four-component reaction by treating ferrocenecarboxylic acid with diverse aldehydes, amines, and isocyanides in methanol solution. Their chemical structures were fully characterized by IR, NMR, HR-MS, and X-ray diffraction analyses. They feature unique molecular morphologies and create a 14-membered ring motif in the centro-symmetric dimers generated in the solid state. Moreover, the electrochemical behavior of these ferrocenyl bis-amides was assessed by cyclic voltammetry.
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11
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Nakao M, Hiroyama Y, Fukayama S, Sano S. N4-methylation changes the conformation of (3S,6S)-3-alkyl-6-benzylpiperazine-2,5-diones from folded to extended. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Aβ1-25-Derived Sphingolipid-Domain Tracer Peptide SBD Interacts with Membrane Ganglioside Clusters via a Coil-Helix-Coil Motif. Int J Mol Sci 2015; 16:26318-32. [PMID: 26540054 PMCID: PMC4661814 DOI: 10.3390/ijms161125955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/19/2015] [Accepted: 10/22/2015] [Indexed: 12/30/2022] Open
Abstract
The Amyloid-β (Aβ)-derived, sphingolipid binding domain (SBD) peptide is a fluorescently tagged probe used to trace the diffusion behavior of sphingolipid-containing microdomains in cell membranes through binding to a constellation of glycosphingolipids, sphingomyelin, and cholesterol. However, the molecular details of the binding mechanism between SBD and plasma membrane domains remain unclear. Here, to investigate how the peptide recognizes the lipid surface at an atomically detailed level, SBD peptides in the environment of raft-like bilayers were examined in micro-seconds-long molecular dynamics simulations. We found that SBD adopted a coil-helix-coil structural motif, which binds to multiple GT1b gangliosides via salt bridges and CH–π interactions. Our simulation results demonstrate that the CH–π and electrostatic forces between SBD monomers and GT1b gangliosides clusters are the main driving forces in the binding process. The presence of the fluorescent dye and linker molecules do not change the binding mechanism of SBD probes with gangliosides, which involves the helix-turn-helix structural motif that was suggested to constitute a glycolipid binding domain common to some sphingolipid interacting proteins, including HIV gp120, prion, and Aβ.
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14
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Lim CW. π-Box Molecule: Complexation Study for Flexible Fatty Acid Alkyl Chains in Water. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Choon Woo Lim
- Department of Chemistry, College of Life Science and Nano-technology; Hannam University; Daejeon 305-811 Republic of Korea
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15
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Shao GK, Zhao M, Wei Z, Ma JP, Guo DS. Two novel ferrocenyl dipeptide-like compounds generated via the Ugi four-component reaction. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2015; 71:667-72. [PMID: 26243412 DOI: 10.1107/s2053229615012322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 06/26/2015] [Indexed: 11/11/2022]
Abstract
The Ugi four-component reaction, a powerful method for the synthesis of diverse dipeptide-like derivatives in combinatorial chemistry, was used to synthesize (S)-1'-{N-[1-(anthracen-9-yl)-2-(tert-butylamino)-2-oxoethyl]-N-(4-methoxyphenyl)carbamoyl}ferrocene-1-carboxylic acid dichloromethane disolvate, [Fe(C6H5O2)(C33H31N2O3)]·2CH2Cl2, (I), and (S)-2-(anthracen-9-yl)-N-tert-butyl-2-[N-(4-methylphenyl)ferrocenylformamido]acetamide, [Fe(C5H5)(C33H31N2O2)], (II). They adopt broadly similar molecular conformations, with near-eclipsed cyclopentadienyl rings and near-perpendicular amide planes in their dipeptide-like chains, one of which is almost coplanar with its attached cyclopentadienyl ring but perpendicular to the aromatic ring bound to the N atom. In the supramolecular structure of (I), a two-dimensional network is constructed based on molecular dimers and a combination of intermolecular O-H···O, N-H···O and C-H···O hydrogen bonds, forming R2(2)(11), R2(2)(16), R2(2)(22) and C(9) motifs. These two-dimensional networks are connected by C-H···O and C-H···Cl contacts to create a three-dimensional framework, where one dichloromethane solvent molecule acts as a bridge between two neighbouring networks. In the packing of (II), classical hydrogen bonds are absent and an infinite one-dimensional chain is generated via a combination of C-H···O hydrogen bonds and C-H···π interactions, producing a C(7) motif. This work describes a simple synthesis and the supramolecuar structures of ferrocenyl dipeptide-like compounds and is significant in the development of redox-active receptors.
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Affiliation(s)
- Guang-Kui Shao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Mei Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zheng Wei
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Jian-Ping Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Dian-Shun Guo
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Shandong Normal University, Jinan 250014, People's Republic of China
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Barman A, Batiste B, Hamelberg D. Pushing the Limits of a Molecular Mechanics Force Field To Probe Weak CH···π Interactions in Proteins. J Chem Theory Comput 2015; 11:1854-63. [DOI: 10.1021/ct501036r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Arghya Barman
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Bruce Batiste
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department
of Chemistry and
the Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30302-3965, United States
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18
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Chang YY, Ho TL, Chung WS. Deformative transition of the Menschutkin reaction and helical atropisomers in a congested polyheterocyclic system. J Org Chem 2014; 79:9970-8. [PMID: 25279831 DOI: 10.1021/jo501815y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 4,7-phenanthroline polycyclic 1A designed for probing the limits of the Menschutkin reaction was synthesized in a six-step sequence. The rotational barrier of the phenyl ring nearby the N-methyl group in rac-2A was estimated to be ≫ 18.1 kcal/mol from VT-NMR experiments, making them a new type of helical atropisomer. The methylation rate constants of 9 and 1A with MeI was found to be 2.22 × 10(-4) and 9.62 × 10(-6) s(-1) mol(-1) L, respectively; thus, the formation rate of (P/M)-2A is one of the slowest rates ever reported for a Menschutkin reaction. The N-methyl protons in (P/M)-2A exhibit a significant upfield shift (Δδ 1.0 ppm) in its (1)H NMR, compared to those without a nearby phenyl, indicating a strong CH-π interaction is involved. Conformational flexibility in dipyridylethene 9 is clearly shown by its complexation with BH3 to form helical atropisomers (P,P/M,M)-10. The pKa values of the conjugate acids of 1A and 9 in acetonitrile were determined to be 4.65 and 5.07, respectively, which are much smaller compared to that of pyridine 14a (pKa = 12.33), implying that the basicity, nucleophilicity, and amine alkylation rates of 1A and 9 are markedly decreased by the severe steric hindrance of the flanking phenyl rings in the polyheterocycles.
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Affiliation(s)
- Yung-Yu Chang
- Department of Applied Chemistry, National Chiao-Tung University , Hsinchu 30050, Taiwan-ROC
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19
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Pandey AK, Thomas KM, Forbes C, Zondlo NJ. Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix. Biochemistry 2014; 53:5307-14. [PMID: 25075447 PMCID: PMC4139158 DOI: 10.1021/bi500696k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Indexed: 01/10/2023]
Abstract
Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic-proline interactions, C-H/π interactions between the aromatic π face and proline ring C-H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic-proline interactions (aromatic-cis-proline and proline-cis-proline-aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis-trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline-aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.
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Affiliation(s)
- Anil K. Pandey
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Krista M. Thomas
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina
R. Forbes
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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20
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Zhao C, Li P, Smith MD, Pellechia PJ, Shimizu KD. Experimental Study of the Cooperativity of CH−π Interactions. Org Lett 2014; 16:3520-3. [DOI: 10.1021/ol5014729] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Chen Zhao
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ping Li
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department
of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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21
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Nakao M, Toriuchi Y, Fukayama S, Sano S. Synthesis and Conformational Characterization of Diketopiperazines Bearing a Benzyl Moiety. CHEM LETT 2014. [DOI: 10.1246/cl.131001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Michiyasu Nakao
- Graduate School of Pharmaceutical Sciences, The University of Tokushima
| | - Yuriko Toriuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokushima
| | - Shintaro Fukayama
- Graduate School of Pharmaceutical Sciences, The University of Tokushima
| | - Shigeki Sano
- Graduate School of Pharmaceutical Sciences, The University of Tokushima
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22
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C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability. J Mol Model 2014; 20:2136. [DOI: 10.1007/s00894-014-2136-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/02/2014] [Indexed: 11/25/2022]
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23
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Bagdi PR, Basha RS, Baruah PK, Khan AT. Copper oxide nanoparticle mediated ‘click chemistry’ for the synthesis of mono-, bis- and tris-triazole derivatives from 10,10-dipropargyl-9-anthrone as a key building block. RSC Adv 2014. [DOI: 10.1039/c3ra44869j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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24
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Abstract
β-lactam group of antibiotics is the most widely used therapeutic molecules for treating bacterial infections. The main mode of bacterial resistance to β-lactams is by β-lactamases. In the present study, we report our results on the role of cation-π interactions in β-lactamases and their environmental preferences. The number of interactions formed by arginine is higher than lysine in the cationic group, while tyrosine is comparatively higher than phenylalanine and tryptophan in the π group. Our results indicate that cation-π interactions might play an important role in the global conformational stability of β-lactamases.
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25
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Abstract
Proline residues have unique roles in protein folding, structure, and function. Proline and the aromatic amino acids comprise the encoded cyclic protein residues. Aromatic protein side chains are defined by their negatively charged π faces, while the faces of the proline ring are partially positively charged. This polarity results from their two-point connection of the side chain to the electron-withdrawing protein backbone, and the lower electronegativity of hydrogen compared to carbon, nitrogen, and oxygen. The hydrogens adjacent to the carbonyl and amide nitrogen, Hα and Hδ, respectively, are the most partially positive. Proline's side chain is also conformationally restricted, allowing for interaction with aromatic residues with minimal entropic or steric penalty. Proline and aromatic residues can interact favorably with each other, due to both the hydrophobic effect and the interaction between the π aromatic face and the polarized C-H bonds, called a CH/π interaction. Aromatic-proline interactions can occur locally, for example, to stabilize cis-amide bonds, and over larger distances, in the tertiary structures of proteins, and intermolecularly in protein-protein interactions. In peptides and proteins, aromatic-proline sequences more readily adopt cis-prolyl amide bonds, where the aromatic ring interacts with the proline ring in the cis conformation. In aromatic-proline sequences, Trp and Tyr are more likely to induce cis-amide bonds than Phe, suggesting an aromatic electronic effect. This result would be expected for a CH/π interaction, in which a more electron-rich aromatic would have a stronger (more cis-stabilizing) interaction with partial positive charges on prolyl hydrogens. In this Account, we describe our investigations into the nature of local aromatic-proline interactions, using peptide models. We synthesized a series of 26 peptides, TXPN, varying X from electron-rich to electron poor aromatic amino acids, and found that the population of cis-amide bond (Ktrans/cis) is tunable by aromatic electronics. With 4-substituted phenylalanines, we observed a Hammett correlation between aromatic electronics and Ktrans/cis, with cis-trans isomerism electronically controllable by 1.0 kcal/mol. All aromatic residues exhibit a higher cis population than Ala or cyclohexylalanine, with Trp showing the strongest aromatic-proline interaction. In addition, proline stereoelectronic effects can modulate cis-trans isomerism by an additional 1.0 kcal/mol. The aromatic-proline interaction is enthalpic, consistent with its description as a CH/π interaction. Proline-aromatic sequences can also promote cis-prolyl bonds, either through interactions of the aromatic ring with the preceding cis-proline or with the Hα prior to cis-proline. Within proline-rich peptides, sequences commonly found in natively disordered proteins, aromatic residues promote multiple cis-amide bonds due to multiple favorable aromatic-proline interactions. Collectively, we found aromatic-proline interactions to be significantly CH/π in nature, tunable by aromatic electronics. We discuss these data in the context of aromatic-proline and aromatic-glycine interactions in local structure, in tertiary structure, in protein-protein interactions, and in protein assemblies.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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26
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Computational study on C−H…π interactions of acetylene with benzene, 1,3,5-trifluorobenzene and coronene. J Mol Model 2012; 19:2855-64. [DOI: 10.1007/s00894-012-1729-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 11/12/2012] [Indexed: 11/25/2022]
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27
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Zhao C, Parrish RM, Smith MD, Pellechia PJ, Sherrill CD, Shimizu KD. Do Deuteriums Form Stronger CH−π Interactions? J Am Chem Soc 2012; 134:14306-9. [DOI: 10.1021/ja305788p] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chen Zhao
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Robert M. Parrish
- School of Chemistry and Biochemistry
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Mark D. Smith
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - C. David Sherrill
- School of Chemistry and Biochemistry
and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332,
United States
| | - Ken D. Shimizu
- Department of Chemistry and
Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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29
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Ganguly HK, Majumder B, Chattopadhyay S, Chakrabarti P, Basu G. Direct Evidence for CH···π Interaction Mediated Stabilization of Pro-cisPro Bond in Peptides with Pro-Pro-Aromatic motifs. J Am Chem Soc 2012; 134:4661-9. [DOI: 10.1021/ja209334v] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Himal K. Ganguly
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Barun Majumder
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Sarbani Chattopadhyay
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Pinak Chakrabarti
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Gautam Basu
- Department
of Biophysics and ‡Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India
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30
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RAMANATHAN K, SETHUMADHAVAN RAO. EXPLORING THE ROLE OF C–H … π INTERACTIONS ON THE STRUCTURAL STABILITY OF ANTIMICROBIAL PEPTIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005155] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A computational analysis on the C – H … π interactions in a group of 53 antimicrobial peptides was investigated. A total of 162 C – H … π interactions were observed. Side-chain to side-chain C – H … π interactions are the predominant type of interactions in antimicrobial peptides data set. There was an average of one significant C – H … π interaction for every 7 residues in the antimicrobial peptides investigated. Long-range C – H … π interactions are the predominant type of interactions. The secondary structure preference, solvent accessibility and stabilization centers of these of C – H … π interacting residues were estimated. It is likely that the C – H … π interactions contribute significantly to the overall stability of antimicrobial peptides. These interactions were observed after a molecular dynamics study on these set of antimicrobial peptides using CHARMM force field.
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Affiliation(s)
- K. RAMANATHAN
- School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - RAO SETHUMADHAVAN
- School of Biotechnology, Chemical and Biomedical Engineering, Bioinformatics Division, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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31
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Carroll WR, Zhao C, Smith MD, Pellechia PJ, Shimizu KD. A Molecular Balance for Measuring Aliphatic CH−π Interactions. Org Lett 2011; 13:4320-3. [DOI: 10.1021/ol201657p] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- William R. Carroll
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Chen Zhao
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Mark D. Smith
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Perry J. Pellechia
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ken D. Shimizu
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
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32
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The square conformation of phenylglycine-incorporated ascidiacyclamide is stabilized by CH/π interactions between amino acid side chains. Bioorg Med Chem 2011; 19:3372-7. [DOI: 10.1016/j.bmc.2011.04.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/14/2011] [Accepted: 04/18/2011] [Indexed: 11/20/2022]
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33
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Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 617] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
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34
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 495] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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35
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Gao H. Theoretical characterization of hole mobility in N,N′-diphenyl-N,N′-bis(3-methylphenyl)-(1,1′-biphenyl)-4,4′-diamine. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.09.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Guimarães DO, Borges WS, Vieira NJ, de Oliveira LF, da Silva CHTP, Lopes NP, Dias LG, Durán-Patrón R, Collado IG, Pupo MT. Diketopiperazines produced by endophytic fungi found in association with two Asteraceae species. PHYTOCHEMISTRY 2010; 71:1423-1429. [PMID: 20541231 DOI: 10.1016/j.phytochem.2010.05.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Revised: 05/07/2010] [Accepted: 05/11/2010] [Indexed: 05/29/2023]
Abstract
Diketopiperazine (DKP) derivatives, named colletopiperazine, fusaperazine C and E as well as four known DKPs were isolated from cultures of Colletotrichum gloeosporioides, Penicillium crustosum, both endophytic fungi isolated from Viguiera robusta, and a Fusarium spp., an endophyte of Viguiera arenaria, respectively. Their structures were established on the basis of their spectroscopic data. Conformational analysis of two known DKPs showed that folded conformations were as energetically stable as the extended one.
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Affiliation(s)
- Denise O Guimarães
- Departamento de Ciências Farmacêuticas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café s/n, 14040-903 Ribeirão Preto, SP, Brazil
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37
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Batulan Z, Haddad GA, Blunck R. An intersubunit interaction between S4-S5 linker and S6 is responsible for the slow off-gating component in Shaker K+ channels. J Biol Chem 2010; 285:14005-19. [PMID: 20202932 DOI: 10.1074/jbc.m109.097717] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Voltage-gated ion channels are controlled by the membrane potential, which is sensed by peripheral, positively charged voltage sensors. The movement of the charged residues in the voltage sensor may be detected as gating currents. In Shaker K(+) channels, the gating currents are asymmetric; although the on-gating currents are fast, the off-gating currents contain a slow component. This slow component is caused by a stabilization of the activated state of the voltage sensor and has been suggested to be linked to ion permeation or C-type inactivation. The molecular determinants responsible for the stabilization, however, remain unknown. Here, we identified an interaction between Arg-394, Glu-395, and Leu-398 on the C termini of the S4-S5 linker and Tyr-485 on the S6 of the neighboring subunit, which is responsible for the development of the slow off-gating component. Mutation of residues involved in this intersubunit interaction modulated the strength of the associated interaction. Impairment of the interaction still led to pore opening but did not exhibit slow gating kinetics. Development of this interaction occurs under physiological ion conduction and is correlated with pore opening. We, thus, suggest that the above residues stabilize the channel in the open state.
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Affiliation(s)
- Zarah Batulan
- Département de Physique and Groupe d'Etude des Protéines Membranaires, Université de Montréal, Montréal, Quebec H3C 3J7 Canada
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38
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Wei MY, Liu Z, Zhang XL, Shao CL, Wang CY. Methyl 3-hydr-oxy-4-(3-methyl-but-2-en-yloxy)benzoate. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o734-5. [PMID: 21582468 PMCID: PMC2968826 DOI: 10.1107/s160053680900806x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 03/05/2009] [Indexed: 11/19/2022]
Abstract
The title compound, C13H16O4, was isolated from culture extracts of the endophytic fungus Cephalosporium sp. The ester and ether substituents are twisted only slightly out of the benzene ring plane, making dihedral angles of 2.16 (2) and 3.63 (5)°, respectively. The non-H atoms of all three substituents are almost coplanar with the benzene ring, with an r.m.s. deviation of 0.0284 Å from the mean plane through all non-H atoms in the structure. A weak intramolecular O—H⋯O hydrogen bond contributes to this conformation. In the crystal structure, molecules are linked into a one-dimensional chain by intermolecular O—H⋯O hydrogen bonds. Weak non-classical C—H⋯π contacts are also observed in the structure.
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39
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Takahashi O, Yamasaki K, Kohno Y, Ueda K, Suezawa H, Nishio M. The Origin of the Relative Stability of Axial Conformers of Cyclohexane and Cyclohexanone Derivatives: Importance of the CH/n and CH/π Hydrogen Bonds. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2009. [DOI: 10.1246/bcsj.82.272] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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41
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Deng D, Liu P, Fu W, Ji B. (2R,3R)-2-[(4-Chloro-phen-yl)hydroxy-meth-yl]cyclo-penta-none. Acta Crystallogr Sect E Struct Rep Online 2008; 65:o164-5. [PMID: 21581621 PMCID: PMC2968076 DOI: 10.1107/s160053680804261x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 12/15/2008] [Indexed: 11/18/2022]
Abstract
The title compound, C12H13ClO2, was prepared by the direct asymmetric intermolecular aldol reaction of cyclopentanone and 4-chlorobenzaldehyde catalysed by l-tryptophan in water. The absolute molecular structure was determined to be a racemic twin with 91% (2R,3R) isomer and 9% of the (2S,3S) form. In the crystal structure, the molecules are connected into a one-dimensional chain along the a axis through the formation of intermolecular O—H⋯O hydrogen bonds. Further, non-conventional C—H⋯O and C—H⋯π contacts are observed in the structure, which consolidate the crystal packing.
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42
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Di Tommaso D, French SA, Zanotti-Gerosa A, Hancock F, Palin EJ, Catlow CRA. Computational Study of the Factors Controlling Enantioselectivity in Ruthenium(II) Hydrogenation Catalysts. Inorg Chem 2008; 47:2674-87. [DOI: 10.1021/ic701981v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Devis Di Tommaso
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Samuel A. French
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Antonio Zanotti-Gerosa
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Fred Hancock
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - Erika J. Palin
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
| | - C. Richard A. Catlow
- Davy Faraday Research Laboratory, Kathleen Lonsdale Building, University College of London, Gower Street, London WC1E 6BT, United Kingdom, and Christopher Ingold Laboratories, Department of Chemistry, University College of London, 20 Gordon Street, London WC1H OAJ, United Kingdom, Johnson Matthey Technology Centre, Blount’s Court, Sonning Common, RG4 9NH, United Kingdom, Johnson Matthey Catalysis and Chiral Technologies, 28 Cambridge Science Park, Milton Road, Cambridge, CB4 0FP, United Kingdom
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The conformation of alkyl cyclohexanones and terpenic ketones. Interpretation for the ‘alkylketone effect’ based on the CH/π(CO) hydrogen bond. Tetrahedron 2008. [DOI: 10.1016/j.tet.2007.12.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Sureshan KM, Uchimaru T, Yao Y, Watanabe Y. Strength from weakness: CH⋯π stabilized conformational tuning of benzyl ethers and a consequent co-operative edge-to-face CH⋯π network. CrystEngComm 2008. [DOI: 10.1039/b718099c] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Anbarasu A, Anand S, Babu MM, Sethumadhavan R. Investigations on C–H⋯π interactions in RNA binding proteins. Int J Biol Macromol 2007; 41:251-9. [PMID: 17420044 DOI: 10.1016/j.ijbiomac.2007.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2006] [Revised: 02/26/2007] [Accepted: 02/27/2007] [Indexed: 10/23/2022]
Abstract
We have investigated the roles played by C-Hcdots, three dots, centeredpi interactions in RNA binding proteins. There was an average of 55 C-Hcdots, three dots, centeredpi interactions per protein and also there was an average of one significant C-Hcdots, three dots, centeredpi interaction for every nine residues in the 59 RNA binding proteins studied. Main-chain to side-chain C-Hcdots, three dots, centeredpi interactions is the predominant type of interactions in RNA binding proteins. The donor atom contribution to C-Hcdots, three dots, centeredpi interactions was mainly from Phe, Tyr, Trp, Pro, Gly, Lys, His and Ala residues. The acceptor atom contribution to main-chain to side-chain C-Hcdots, three dots, centeredpi and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions was mainly from Phe and Tyr residues. On the contrary, the acceptor atoms of Trp residues contributed to all the four types of C-Hcdots, three dots, centeredpi interactions. Also, Trp contributed both donor and acceptor atoms in main-chain to side-chain, main-chain to side-chain five-member aromatic ring and side-chain to side-chain C-Hcdots, three dots, centeredpi interactions. The secondary structure preference analysis of C-Hcdots, three dots, centeredpi interacting residues showed that, Arg, Gln, Glu, His, Ile, Leu, Lys, Met, Phe and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Trp and Val preferred to be in strand conformation. Long-range C-Hcdots, three dots, centeredpi interactions are the predominant type of interactions in RNA binding proteins. More than 50% of C-Hcdots, three dots, centeredpi interacting residues had a higher conservation score. Significant percentage of C-Hcdots, three dots, centeredpi interacting residues had one or more stabilization centers. Seven percent of the theoretically predicted stabilizing residues were also involved in C-Hcdots, three dots, centeredpi interactions and hence these residues may also contribute additional stability to RNA binding proteins.
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Affiliation(s)
- Anand Anbarasu
- School of Bio-Technology, Chemical and Bio-Medical Engineering, VIT University, Vellore 632014, India
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Takahashi O, Yamasaki K, Kohno Y, Ueda K, Suezawa H, Nishio M. Origin of the π-Facial Stereoselectivity in the Addition of Nucleophilic Reagents to Chiral Aliphatic Ketones as Evidenced by High-Level Ab Initio Molecular-Orbital Calculations. Chem Asian J 2006; 1:852-9. [PMID: 17441128 DOI: 10.1002/asia.200600204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ab initio molecular-orbital (MO) calculations were carried out, at the MP2/6-311++G(d,p)//MP2/6-31G(d) level, to investigate the conformational Gibbs energy of alkyl 1-cyclohexylethyl ketones, cyclo-C6H11CHCH3-CO-R (R = Me, Et, iPr, and tBu). In each case, one of the equatorial conformations was shown to be the most stable. Conformers with the axial CHCH3COR group were also shown to be present in an appreciable concentration. Short C-H...C=O and C-H...O=C distances were found in each stable conformation. The result was interpreted on the grounds of C-H...pi(C=O) and C-H...O hydrogen bonds, which stabilize the geometry of the molecule. The ratio of the diastereomeric secondary alcohols produced in the nucleophilic addition to cyclo-C6H11CHCH3-CO-R was estimated on the basis of the conformer distribution. The calculated result was consistent with the experimental data previously reported: the gradual increase in the product ratio (major/minor) along the series was followed by a drop at R = tBu. The energy of the diastereomeric transition states in the addition of LiH to cyclo-C6H11CHCH3-CO-R was also calculated for R = Me and tBu. The product ratio did not differ significantly in going from R = Me to tBu in the case of the aliphatic ketones. This is compatible with the above result calculated on the basis of the conformer distribution. Thus, the mechanism of the pi-facial selection can be explained in terms of the simple premise that the geometry of the transition state resembles the ground-state conformation of the substrates and that the nucleophilic reagent approaches from the less-hindered side of the carbonyl pi face.
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Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
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Katragadda M, Magotti P, Sfyroera G, Lambris JD. Hydrophobic effect and hydrogen bonds account for the improved activity of a complement inhibitor, compstatin. J Med Chem 2006; 49:4616-22. [PMID: 16854067 DOI: 10.1021/jm0603419] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophans at positions 4 and 7 of compstatin, a peptide complement inhibitor, are crucial for its interaction with C3. However, the nature of their involvement has not been studied to date. Here we investigate the molecular forces involved in the C3-compstatin interactions, mediated by aromatic residues, by incorporating in these two positions various tryptophan analogues (5-methyltryptophan, 5-fluorotryptophan, 1-methyltryptophan, and 2-naphthylalanine) and assessing the resulting peptides for activity by enzyme-linked immunosorbent assay (ELISA) and binding by isothermal titration calorimetry (ITC). Of all the compstatin analogues, peptides containing 1-methyltryptophan at position 4 exhibited the highest binding affinity (Kd = 15 nM) and activity (IC50 = 0.205 microM), followed by a peptide containing 5-fluorotryptophan at position 7. Our observations suggest that hydrophobic interactions involving residues at position 4 and the hydrogen bond initiated by the indole nitrogen are primarily responsible and crucial for the increase in activity. These findings have important implications for the design of clinically useful complement inhibitors.
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Affiliation(s)
- Madan Katragadda
- Protein Chemistry Laboratory, Department of Pathology & Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Ringer AL, Figgs MS, Sinnokrot MO, Sherrill CD. Aliphatic C−H/π Interactions: Methane−Benzene, Methane−Phenol, and Methane−Indole Complexes. J Phys Chem A 2006; 110:10822-8. [PMID: 16970377 DOI: 10.1021/jp062740l] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Noncovalent C-H/pi interactions are prevalent in biochemistry and are important in molecular recognition. In this work, we present potential energy curves for methane-benzene, methane-phenol, and methane-indole complexes as prototypes for interactions between C-H bonds and the aromatic components of phenylalanine, tyrosine, and tryptophan. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for selected complex configurations. Using corrections for higher-order electron correlation determined with coupled-cluster theory through perturbative triples [CCSD(T)] in the aug-cc-pVDZ basis set, we estimate, through an additive approximation, results at the very accurate CCSD(T)/aug-cc-pVTZ level of theory. Symmetry-adapted perturbation theory (SAPT) is employed to determine the physically significant components of the total interaction energy for each complex.
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Affiliation(s)
- Ashley L Ringer
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Ran J, Wong MW. Saturated Hydrocarbon−Benzene Complexes: Theoretical Study of Cooperative CH/π Interactions. J Phys Chem A 2006; 110:9702-9. [PMID: 16884202 DOI: 10.1021/jp0555403] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-level ab initio calculations at the CCSD(T)/aug-cc-pVTZ//MP2/aug(d,p)-6-311G(d,p) level were employed to investigate the cooperative CH/pi effects between the pi face of benzene and several modeled saturated hydrocarbons, propane, isobutane, cyclopropane, cyclobutane, cyclopentane, cyclohexane, cyclopentane, cyclooctane, and bicyclo[2.2.2]octane. In all cases, multiple C-H groups (2-4) are found to interact with the pi face of benzene, with one C-H group pointing close to the center of the benzene ring. The geometries of these complexes are governed predominantly by electrostatic interaction between the interacting systems. The calculated interaction energies (10-14 kJ mol(-1)) are 2-3 times larger than that of the prototypical methane-benzene complex. The trends of geometries, interaction energies, binding properties, as well as electron-density topological properties were analyzed. The calculated interaction energies correlate well with the polarizabilities of the hydrocarbons. AIM analysis confirms the hydrogen-bonded nature of the CH/pi interactions. Significant changes in proton chemical shift and stretching frequency (blue shift) are predicted for the ring C-H bond in these complexes.
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Affiliation(s)
- Jiong Ran
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore 117543
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